The City of Atlantis (Built in Lego Bricks), located on the Planet of Lantea, in the Pegasus Galaxy, was built by the ancient race known as the Atlanteans. Built millions of years ago on the planet Earth, in Antarctica, the city used it's "Stardrive", a city wide engine, to flee to Lantea, after a massive plague broke out in the Milky Way, leaving behind a small outpost in present day Antartica, named Terra Atlantis, and one on the Planet of Proclarush, and named the outpost Taonas. After the city had been relocated to Lantea, the people renamed themselves the "Atlanteans" after their new planet. The Atlanteans, builders of the famous Stargate network, created a new network of Stargates in the Pegasus Galaxy, and also installed a city wide shield and bank of GateShips (AKA Jumpers) into the city, powered by ZPMS, harnessing the energy by Zero Point Energy. The Atlanteans also installed Drone Weapons, powerful explosives into several areas of the city in case of Attack. Soon, the Atlanteans colonized many worlds, such as Taranis, a drydock for Massive Aurora Class Ships, connected to Atlantis by the Stargate network.

Inside Atlantis, there are many, many rooms, including dormitories, the Stargate Room, the Control Center, and GateShip bays, to name a few. To accomodate the massive population in Atlantis, hundreds of dormitorial rooms exist throughout the city, and several, such as those of the High Council, governing body of Atlantis, have more spacious quarters. The Stargate Room, located in the central spire of the city, is a large and spacious room accomodating the Atlantis Stargate, equipped with a shield to prevent matter re-enrty, and the Atlantis Stargate is the only one able to dial to Earth, and other galaxies. The Stargate Room is seperated from the control room by a large flight of stairs, leading to the Transporters and Control Room. The Control, a spacious room, accomodates all of Atlantis's controls, sensors, systems, and Stargate, and located next to the Confrence Rooms, where diplomatic meetings were held 10,000 years ago. Another room in Atlantis, the Holographic Room, has all of the city's history stored in it, and all with the ATA (Ancient Technology Activation Gene) can access, provided by large amounts of power, however! The central spire of Atlantis, also contains the GateShip Bay, directly above the Stargate Room and Control Center, and the highest point in the building, and contains a number of ships, capable of traveling through the Stargate. Another GateShip bay, located under Atlantis's water line, exists so the Ships can pilot underwater, acting like Submersibles to a certain depths. Another room in the city, the Zero Point Module Power Outlet, contains the 3 ZPMS to power the city at full power capacity, and controlled by a console next to the outlet. This room is located at the base of the Central Spire. Atlantis also contains a brig to keep captives away from the general population, and a Atlantean Chair Room for Powering the Drone Weapons (See Atlantean Technology) and for Piloting the city while using the Star Drive, though this can be done from the Auxilary Control Room, below the city's waterline. Also, in the City, many laboratories for studying Asencion, the process by which one becomes pure energy, a laboratory for studying animals, and several stasis laboratories exist within the city's walls. The City of Atlantis also has several types of sensors: Biometric Sensors, Long Range Sensors, and Internal Sensors, used to scan inside Atlantis. Atlantis also has an extensive medical laboratory for treating the sick.

Several years after their arrival in the Pegasus Galaxy, the Atlanteans started to seed worlds with humans, populating them and filling the galaxy with more intelligent beings, but this soon gave rise to the Wraith, half human, half "Iratus" Bug, hybrids, that fed quickly upon the Galaxy's human population and soon threatened the Atlanteans and Hoffans, Dorandans, Athosians, Humans and Taranians.

The Wraith-Atlantean War, which lasted 100 Long Years, was believed to have started when the Wraith evolved and claimed equal intelligence with the Atlanteans, forming disputes, and when Atlantis sent diplomats to the Wraith World, and they were killed, sparking the start of the War, which the Atlanteans seemed to be winning from the beginning with their impressive technology dominating over that of the Wraith with their Hive Ships and Dart Fighters. When the Wraith started to grow, mysteriously, and overpowered the Atlanteans at several of their strongholds, including Taranis, halting the construction of the Hippofroalcus, an Aurora Class Warship; Athos, forcing the Athosians of Taverly into hiding; leveling Hoff; destroying Doranda, location of the Project Arcturus Experiment, and attempted to even destroy Atlantis itself, though unsucessful and devestating, with it's Drone Weapons, Shields, and Satellites, the Wraith kept fighting, destroying a Passsenger Ship Attempting to flee the Lantea System, and forcing the High Council to Sink the city under the Lantean Oceans, and flee back to Terra Earth, and hope one day, the Atlanteans would one day return and continue the legacy the Original Atlanteans left behind.

Early in 2004, after the discovery of the Proclarush Taonas and Antarctic outposts, the people of Stargate Command on Earth were able to discover the Stargate Address to Atlantis. However, Atlantis was believed to be millions of light years away, and in the Pegasus Galaxy, and required a ZPM to power their Stargate. After successfully dialing Atlantis, the SGC sent their most talented soldiers, doctors, scientists and civilian staff, and it included the brilliant Dr. Rodney McKay, a scientist in astrophysics, Colonel John Sheppard of the USAF, Dr. Carson Beckett, and amazing Scottish Doctor, and Dr. Elizabeth Weir, to lead the expedition. Upon their arrival to the lost city of the Ancients, the city's shield began to collapse, having sustained itself underwater for 10,000 years, and the city rose to the surface of Lantea once again. Hoping to meet many friendly Pegasus Galaxy cultures, Atlantis 1, which consisted of John Sheppard, Rodney McKay, and Aiden Ford, dialed Athos, and learned of the Wraith from it's native people, and met their leader, Teyla Emmagen, whi joined the Atlantis Staff. Soon after their arrival on Athos, a Wraith Culling began. The people were evacuated to Atlantis, and more adventures began. Months passed of exciting news, from finding someone from 10,000 years ago, to meeting more Wraith and the Wraith's attack on Atlantis itself. Once the team disguised the city using a Gateship Cloak, they once again avoided meeting the Wraith. In the next weeks, the team met the evil Genii, and the primitive society on Taranis, former colony, and found an Aurora class battleship, the Hippofroalcus, and avoided the eruption of a Supervolcano on the planet's surface. Dr. Beckett even engineered a serum to turn Wraith to humans, and tested it on Michael, a scientist, who eventually turned on the AE and the Wraith, abducting the Athosian people and turning them into Wraith-Athosian hybrids. The expedition also avoided a massive hurricane hitting the city, and avoided and massive solar flare from destroying Lantea. A Year later, the expedition stumbled across Asuras, home of the Asuran Replicators, and discovered their evil and awful nature of hating the Atlanteans for their treatment of them, and attempted to destroy Atlantis using their own city ship. The AE responded by delivering nuclear warheads to the Asuran Shipyards, and the Asurans avenged them by attempting to destroy atlantis, once again, but with a laser. The AE was forced to sink the city underwater, but the beam still cut through to the city's shield. Dr. McKay and Dr. Weir decided to power the city's Stardrive and leave Lantea, and were successful, but the beam hit the Central Spire and injured Ronon Dex and Elizabeth Weir, and forced McKay to reactivate the Nanite Cells in her body. Soon, the city dropped out of Hyperspace prematurely, and the Ae were forced to raid Asuras for it' ZPM to safely relocate Atlantis. The team suceeded in gaining the ZPM, but also in reactivating the Wraith Attack code in the Asurans, and let them fight the Wraith. With the Wraith and Asuran numbers dying, the AE mourned the loss of Elizabeth Weir, but welcomed Dr. Samantha Carter, their new leader. More adventures of the AE across the Pegasus revealed Michael's evil plans, and even the kidnapping of Teyla Emmagen.